Hi Waqas,
Before we get off onto a lengthy discussion... You -did- mean 1FA and
not F1A, right? The proper name for the residue is 1FA.
Also, did you try using our builder online to make your complex? Did
you have problems with it? You might find that to be a much easier
way to go. If something didn't work, let us know. We have a mailing
list you can join when you register. Or send email to
glycam.gmail.com if you prefer.
Also, why do you want a frcmod file? If I understand you correctly,
you shouldn't need it for this. The parameter and prep files should
be all you need (for fucose, that is). You can download the latest
versions of the Glycam parameters here:
http://www.glycam.com/gl_params.html
You want Glycam_06.prep and Glycam_06d.dat. For linking to proteins,
you also need the glycam_amino* libraries. The leaprc.Glycam06 might
also be useful to you.
:-) Lachele
On 7/8/08, Waqas Nasir <nasirwaqas1983.yahoo.com> wrote:
>
>
>
>
>
> Hi,
>
> Hope every thing is working fine at your side.
>
> Well, I am a new user of glycam and amber, just a couple of weeks old, and I am trying to do some studies with protein carbohydrate complex.
>
> The complex that I have contains beta-d-galactose and alpha-l-fucose with the protein chain (The trisaccharide resides in the binding pocket of the protein and is not covalently attached to it).
>
> With 2 galactoses one can rename them in the pdb file as 1GB and ZGB (since one galactose has linkage position 1, and the other one has linkage positions 2 and 3) but with fucose I am a bit confused because its not present in the standard glycam04 forcefield. I thought of building that residue with "biomolecule builder" (http://www.glycam.com/CCRC/biombuilder/biomb_index.jsp) but could not find a way to generate the prep & frcmod files for F1A (alpha-l-fucose with linkage position 1) residue that I need. I tried antechamber as well but there I do have some missing parameters.
>
> What I am trying to do now is to find a way to generate the prep and frcmod files for this resiue in order to make it recognized in amber, so that I could rename this residue in pdb file and then load the whole pdb (with protein and carbohydrate) to generate top and crd files.
>
> I appologize if my language is not that proper or clear. I hope that you did understand it. I request you to please let me know if I am on the right track or if there is some problem with my understanding of the subject matter.
>
> I would really appreciate if you could respond.
> Wish you and your team all the best!
>
> Thanks,
> Kind regards,
> Waqas.
>
>
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
2-0263
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Received on Wed Jul 09 2008 - 06:07:42 PDT
